diff --git a/README.md b/README.md index 6d58c654ce41109c125a9a7f276b41bf1608175c..bffde0751334148e9e498286d01485fa2c6dc03e 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,10 @@ This package features a GUI for visualizing behaving larvae and editing discrete behavior tags at each time step. -To run `LarvaTagger.jl`, you will need [`julia>=1.6`](https://julialang.org/downloads/) and some input data files, *e.g.* a `trx.mat` file or a pair of `.spine`/`.outline` files, preferably at a leaf of a directory structure such as `<screen_name>/<genotype@effector>/<protocol>/<date_time>`. +To run `LarvaTagger.jl`, you will need [`julia>=1.6`](https://julialang.org/downloads/) and some input data file, *e.g.* a `trx.mat` file or a pair of `.spine`/`.outline` files, preferably located in a repository with directory structure: `<screen_name>/<genotype@effector>/<protocol>/<date_time>`. -An example install procedure can be found in `scripts/make_demontrator.sh`. +If you are not familiar with Julia, you may appreciate installation helpers such as [JILL.py](https://github.com/johnnychen94/jill.py). +An example install procedure can be found in [`scripts/make_demontrator.sh`](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/blob/main/scripts/make_demonstrator.sh). ## Install diff --git a/scripts/larvatagger.jl b/scripts/larvatagger.jl index 4506d0ca54b434b8cdc0ee503d25ae9ec09e8513..ec839916cd9f96161c3b0f5a072bac9ca78b6666 100755 --- a/scripts/larvatagger.jl +++ b/scripts/larvatagger.jl @@ -38,7 +38,7 @@ function main() if parsed_args["import"] infile = parsed_args["<input-path>"] if !isfile(infile) - @error "File not found" $infile + @error "File not found" infile return end outfile = parsed_args["<output-file>"] @@ -63,7 +63,7 @@ function main() verbose = !parsed_args["--quiet"] infile = parsed_args["<input-path>"] if !isfile(infile) - @error "File not found" $infile + @error "File not found" infile return end if parsed_args["--viewer"] diff --git a/scripts/make_demonstrator.sh b/scripts/make_demonstrator.sh index bdc43a7ba4993e824c32b7c84b7e7da518b285a1..1b2bc86ec6fb07c72d322ea6727b376d47ee117e 100755 --- a/scripts/make_demonstrator.sh +++ b/scripts/make_demonstrator.sh @@ -8,18 +8,18 @@ # Nyx tagging UI, with specific options for our beloved alpha-testers. if ! [ -x ~/.local/bin/julia ]; then -# install Jill with pip +# install JILL with pip python3 -m pip install jill -# install Julia with Jill +# install Julia with JILL python3 -m jill install --confirm fi # make the `julia` command available on the commandline export PATH=~/.local/bin:$PATH # get LarvaTagger.jl source -# (the dev branch is used here for testing before release) +# (the dev branch is used here for pre-release testing purposes) git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger -b dev cd LarvaTagger -# install LarvaTagger.jl +# install LarvaTagger.jl with Pkg julia --project=. -e 'using Pkg; Pkg.instantiate()' if ! [ -x ~/.local/bin/larvatagger.jl ]; then pushd ~/.local/bin @@ -29,9 +29,9 @@ fi # get MaggotUBA source and trained models - open-source part git clone https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA -b 20220418 cd MaggotUBA -# install Poetry +# install Poetry with pip python3 -m pip install poetry -# install MaggotUBA; this step requires access to a private repo; +# install MaggotUBA with Poetry; this step requires access to a private repo; # for a new user with no ssh or gpg keys, this is done logging in with `ssh -A` instead of `su` python3 -m poetry install cd